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Noah Nicolaisen kneels down near a makeshift memorial at the scene of a shooting, in Charleston, S.C., June 18, 2015. A gunman opened fire on Wednesday night at a historic black church killing nine people before fleeing. An intense manhunt was underway on Thursday.TRAVIS DOVE/The New York Times

A church massacre in the heart of the Old South has reopened the most enduring wound in American life: the legacy of slavery.

That wound was already rubbed raw by a series of deaths of black men at the hands of police when Dylann Storm Roof walked into Charleston's Emanuel African Methodist Episcopal Church Wednesday evening. Reports said he sat quietly through a prayer meeting before opening fire, killing six women and three men, including church pastor Clementa Pinckney, a South Carolina state senator.

"I have to do it," Mr. Roof, 21, was reported to have said. "You rape our women and you're taking over our country. And you have to go."

Among the victims were Ethel Lance, 70, and 87-year-old Susie Jackson.

The massacre struck an especially deep chord because it recalled a past of church burnings, killings and kidnappings that terrorized Southern blacks well into the civil rights era.

"The fact that this took place in a black church obviously also raises questions about a dark part of our history," a grim President Barack Obama said Thursday.

Known locally as Mother Emanuel, the Gothic Revival church is home to the oldest black congregation south of Baltimore.

One of its founders, Denmark Vesey, was executed for trying to lead a slave revolt in 1822. Whites burned the church down. Rebuilt after the Civil War, it became a gathering place for civil rights organizers in the 1960s.

Throughout U.S. history, black churches have often been targeted by white supremacists. The bombing of a church in Birmingham, Ala., that killed four young girls shocked the country and helped galvanize the Civil Rights Movement. As recently as 2008, three white men were arrested, soon after the election of Mr. Obama, for setting a mainly black church on fire in Springfield, Mass.

In the case Mother Emanuel, the attack seemed more likely to be the work of a deranged loner than an organized movement.

Mr. Roof's Facebook picture shows a frowning young man with a bowl-shaped haircut. He is wearing a jacket bearing the flags of white-ruled Rhodesia and apartheid-era South Africa.

He was listed as living in Eastover, S.C., a small, mostly black town near Columbia.

Police arrested him during a traffic stop in Shelby, N.C., after a 14-hour manhunt.

Mr. Roof wore a bullet-resistant vest over a white T-shirt, black jeans and brown boots as two police officers walked him through a side door at the Shelby police department and down some stairs to a waiting squad car. He had shackles on his feet, and his hands were cuffed behind his back.

Even if he acted alone, the attack had Americans discussing how much had really changed since they elected their first black president. That breakthrough led to hope for reconciliation between blacks and whites and even a "post-racial" future.

The events of the recent past – from the Florida killing of teenager Trayvon Martin to the upheavel in Ferguson, Mo., to the demonstrations in Baltimore – have cast a shadow over the progress that black Americans have made in everything from high school graduation rates to political representation.

Opinion polling has shown that black Americans are much less positive than whites about the state of race relations and much less willing to trust police.

"Is it really getting better? Because now people are dying. It makes you wonder," said Aposia Singleton, 24, who is black. She came down to the white-washed church at 110 Calhoun Street pushing her infant nephew in a stroller.

She said that at the hospital where she works as a lab technician, white and black employees were hugging each other in the halls after they heard the news. But there were awkward moments in the elevator as black and white found themselves alone together. "It's just a vibe. You don't know what that person's thinking."

Mark Woodruff, 57, a doctor from California visiting Charleston on vacation, formed a ring with his children and grandchildren outside the church to say a prayer.

"It's disappointing to see that racism is still alive in America," said Dr. Woodruff, who is white. "But it's encouraging to see the racial mix here – that people are supportive."

As he spoke, passersby of both races stopped to leave flowers, take pictures and strike up conversations.

"It has no reflection at all on Charleston," said Senam Palmer, 22, a musician, who is black. "It just so happened that one person housed their own personal hatreds."

South Carolina has had its share of recent racial trouble.

It was in North Charleston that Walter Scott was killed on April 4, 2015 – an unarmed black man shot in the back by a North Charleston police officer, Michael Slager, after a routine traffic stop. A witness caught the incident on video.

The race issue threatens to overshadow the last year and a half of Mr. Obama's presidency and could loom over the contest to succeed him. It would be a sad irony if the man whose triumphant election seven years ago raised such bright hopes were to spend his final months in office struggling with a racial crisis.

‎On Thursday, Mr. Obama tried to ‎rekindle hope in the wake of the Charleston attack, speaking of the "outpouring of unity and strength and fellowship and love" in the Southern city.

"Mother Emanuel church and its congregation have risen before – from flames, from an earthquake, from other dark times – to give hope to generations of Charlestonians. And with our prayers and our love – and the buoyancy of hope – it will rise again now as a place of peace."

Hate crimes in the United States

While the death toll made the Charleston attack one of the worst in recent years in the United States, hate crime is far from uncommon, according to experts.

Following is a list of some of the more serious or notorious hate crimes:

Feb. 10, 2015: Three young Muslims were gunned down at an apartment near the University of North Carolina campus in Chapel Hill. A neighbor, Craig Stephen Hicks, is arrested. The killings, which are being investigated as a possible hate crime, sparked an outcry overseas.

April, 2014: Three people were fatally shot to death outside two Jewish centres in Overland Park, Kan. Frazier Glenn Cross, a former senior Ku Klux Klan member who had expressed hatred for Jews, has pleaded not guilty to murder charges. However, all three victims were Christians.

August, 2012: White supremacist Wade Michael Page walked into a Sikh temple in Oak Creek, Wis., and fatally shot six worshippers. Page, who wounded four others, including a policeman, was shot by police in a temple parking lot before killing himself.

February, 2011: A group of white men ambushed and beat James Craig Anderson, a 47-year-old black man, in Jackson, Miss., who died after one of the men ran him over with his truck.

With files from Reuters and other wire services

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